Republic of Ireland international Hoolahan has been linked with a January move to Aston Villa, which would see him reunited with former Norwich boss Paul Lambert.
The Carrow Road board are reportedly unwilling to do business with Lambert, however, due to the acrimonious nature of his departure in 2012, a decision that is thought to have upset Hoolahan.
Hughton insisted the 31-year-old's absence from the team at Goodison Park was purely for tactical reasons - although it backfired as Norwich fell to a 2-0 defeat.
"It was a combination of a few things," the former Newcastle United boss explained.
"I chose on this occasion to go with two up front. There will always be questions on whether you should play one off the front or two up front.
"There's always the argument, whichever way you play it, that you should go the other way, but I thought it was quite brave of us to play two, to try stop them (Everton) playing out from the back.
"Wes, of course, has played in the last couple of league games and was injured for the last game, so he very much came into my thoughts, but I decided to go with the two strikers up top.
"There is no situation, he is a Norwich City player.
"He was very much in my thoughts to play today and is very much a strong part of the squad."
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